1 Packages required

library(dmrseq)

2 BSseq objects

2.1 Negative control

load("./input/bsseq_neg_control.RData")

2.2 Simulated data

load("./input/bsseq_sim_100.RData")

3 DMR files

3.1 Negative control

files.nc <- list.files(path = "./input", pattern = "neg_control.txt", full.names = T)
files.nc <- files.nc[grep(pattern = "anno", x = files.nc, invert = T)]
names(files.nc) <- sapply(files.nc, function(x) strsplit(x, "\\.|/")[[1]][4])

read.nc <- lapply(files.nc, function(x) GRanges(read.delim(x, sep = "\t", stringsAsFactors = F, header = T)))

3.2 Simulated data

anno.sim <- read.table("./input/anno_sim_data.txt.gz", sep = "\t", header = T, stringsAsFactors = F)
files.sim <- list.files(path = "./input", pattern = "sim_data.txt", full.names = T)
files.sim <- files.sim[grep(pattern = "anno", x = files.sim, invert = T)]

names(files.sim) <- sapply(files.sim, function(x) strsplit(x, "\\.|/")[[1]][4])

read.sim <- lapply(files.sim, function(x) {
  a <- read.delim(x, sep = "\t", stringsAsFactors = F, header = T)
  cols <- colnames(a)

  if (length(cols[grep(pattern = "qval", x = cols)]) == 0) {
    return(GRanges(a))
  } else {
    b <- GRanges(a)
    b <- b[b$qval <= 0.05, ]
    return(b)
  }
})

pData(bs.sim$bs) <- anno.sim

4 Annotation Human Genome

anno <- getAnnot("hg19")

5 Regions plot Simulated data

## DMRs
dmrs <- data.frame(bs.sim$gr.dmrs, mncov = bs.sim$dmr.mncov, delta = bs.sim$delta)
dmrs <- GRanges(dmrs[order(dmrs$delta, decreasing = T), ])

## Results to be plotted
n1 <- paste(names(read.sim)[2:5], collapse = " | ")
n1 <- gsub(pattern = "_dmr|_sim_data", replacement = "", x = n1)

n2 <- paste(names(read.sim)[6:9], collapse = " | ")
n2 <- gsub(pattern = "_dmr|_sim_data", replacement = "", x = n2)

n3 <- paste(names(read.sim)[c(1, 10:12)], collapse = " | ")
n3 <- gsub(pattern = "_dmr|_sim_data", replacement = "", x = n3)


for (i in 1:100) {
  n <- paste0("Region", i, ": ", "delta ", round(dmrs$delta[i], 3))

  cat("\n \n")
  cat(paste("##", n))
  cat("\n \n")

  plotDMRs(
    BSseq = bs.sim$bs, regions = dmrs[i, ], testCovariate = "Group",
    compareTrack = GenomicRangesList(read.sim[c(2:5)]), qval = F, stat = F,
    highlightMain = F,
    main = n1
  )

  plotDMRs(
    BSseq = bs.sim$bs, regions = dmrs[i, ], testCovariate = "Group",
    compareTrack = GenomicRangesList(read.sim[c(6:9)]), qval = F, stat = F,
    highlightMain = F,
    main = n2
  )

  plotDMRs(
    BSseq = bs.sim$bs, regions = dmrs[i, ], testCovariate = "Group",
    compareTrack = GenomicRangesList(read.sim[c(1, 10:12)]), qval = F, stat = F,
    highlightMain = F,
    main = n3
  )

  cat("\n \n")
}

5.1 Region1: delta 0.447

5.2 Region2: delta 0.44

5.3 Region3: delta 0.433

5.4 Region4: delta 0.425

5.5 Region5: delta 0.42

5.6 Region6: delta 0.42

5.7 Region7: delta 0.414

5.8 Region8: delta 0.413

5.9 Region9: delta 0.399

5.10 Region10: delta 0.39

5.11 Region11: delta 0.39

5.12 Region12: delta 0.389

5.13 Region13: delta 0.387

5.14 Region14: delta 0.383

5.15 Region15: delta 0.382

5.16 Region16: delta 0.379

5.17 Region17: delta 0.378

5.18 Region18: delta 0.374

5.19 Region19: delta 0.372

5.20 Region20: delta 0.372

5.21 Region21: delta 0.372

5.22 Region22: delta 0.37

5.23 Region23: delta 0.364

5.24 Region24: delta 0.36

5.25 Region25: delta 0.359

5.26 Region26: delta 0.357

5.27 Region27: delta 0.353

5.28 Region28: delta 0.345

5.29 Region29: delta 0.344

5.30 Region30: delta 0.339

5.31 Region31: delta 0.339

5.32 Region32: delta 0.333

5.33 Region33: delta 0.329

5.34 Region34: delta 0.328

5.35 Region35: delta 0.327

5.36 Region36: delta 0.324

5.37 Region37: delta 0.322

5.38 Region38: delta 0.322

5.39 Region39: delta 0.322

5.40 Region40: delta 0.319

5.41 Region41: delta 0.319

5.42 Region42: delta 0.318

5.43 Region43: delta 0.318

5.44 Region44: delta 0.317

5.45 Region45: delta 0.314

5.46 Region46: delta 0.313

5.47 Region47: delta 0.313

5.48 Region48: delta 0.312

5.49 Region49: delta 0.312

5.50 Region50: delta 0.306

5.51 Region51: delta 0.306

5.52 Region52: delta 0.305

5.53 Region53: delta 0.303

5.54 Region54: delta 0.303

5.55 Region55: delta 0.298

5.56 Region56: delta 0.296

5.57 Region57: delta 0.295

5.58 Region58: delta 0.295

5.59 Region59: delta 0.294

5.60 Region60: delta 0.292

5.61 Region61: delta 0.291

5.62 Region62: delta 0.29

5.63 Region63: delta 0.289

5.64 Region64: delta 0.277

5.65 Region65: delta 0.276

5.66 Region66: delta 0.275

5.67 Region67: delta 0.275

5.68 Region68: delta 0.274

5.69 Region69: delta 0.27

5.70 Region70: delta 0.267

5.71 Region71: delta 0.263

5.72 Region72: delta 0.259

5.73 Region73: delta 0.254

5.74 Region74: delta 0.25

5.75 Region75: delta 0.246

5.76 Region76: delta 0.246

5.77 Region77: delta 0.242

5.78 Region78: delta 0.24

5.79 Region79: delta 0.239

5.80 Region80: delta 0.239

5.81 Region81: delta 0.238

5.82 Region82: delta 0.236

5.83 Region83: delta 0.234

5.84 Region84: delta 0.233

5.85 Region85: delta 0.223

5.86 Region86: delta 0.214

5.87 Region87: delta 0.208

5.88 Region88: delta 0.199

5.89 Region89: delta 0.197

5.90 Region90: delta 0.197

5.91 Region91: delta 0.197

5.92 Region92: delta 0.196

5.93 Region93: delta 0.191

5.94 Region94: delta 0.188

5.95 Region95: delta 0.183

5.96 Region96: delta 0.176

5.97 Region97: delta 0.165

5.98 Region98: delta 0.161

5.99 Region99: delta 0.151

5.100 Region100: delta 0.149

6 SessionInfo

devtools::session_info()

## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.1 (2018-07-02)
##  os       Ubuntu 16.04.5 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2019-01-07                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package                * version   date       lib source        
##  AnnotationDbi            1.42.1    2018-10-04 [1] Bioconductor  
##  AnnotationHub            2.12.1    2018-09-05 [1] Bioconductor  
##  annotatr                 1.6.0     2018-10-04 [1] Bioconductor  
##  assertthat               0.2.0     2017-04-11 [1] CRAN (R 3.5.1)
##  backports                1.1.3     2018-12-14 [1] CRAN (R 3.5.1)
##  bibtex                   0.4.2     2017-06-30 [1] CRAN (R 3.5.1)
##  bindr                    0.1.1     2018-03-13 [1] CRAN (R 3.5.1)
##  bindrcpp                 0.2.2     2018-03-29 [1] CRAN (R 3.5.1)
##  Biobase                * 2.40.0    2018-10-04 [1] Bioconductor  
##  BiocGenerics           * 0.26.0    2018-10-04 [1] Bioconductor  
##  BiocInstaller            1.30.0    2018-10-04 [1] Bioconductor  
##  BiocParallel           * 1.14.2    2018-07-08 [1] Bioconductor  
##  biomaRt                  2.36.1    2018-10-29 [1] Bioconductor  
##  Biostrings               2.48.0    2018-10-29 [1] Bioconductor  
##  bit                      1.1-14    2018-05-29 [1] CRAN (R 3.5.1)
##  bit64                    0.9-7     2017-05-08 [1] CRAN (R 3.5.1)
##  bitops                   1.0-6     2013-08-17 [1] CRAN (R 3.5.1)
##  blob                     1.1.1     2018-03-25 [1] CRAN (R 3.5.1)
##  BSgenome                 1.48.0    2018-10-04 [1] Bioconductor  
##  bsseq                  * 1.16.1    2018-06-14 [1] Bioconductor  
##  bumphunter               1.22.0    2018-10-04 [1] Bioconductor  
##  callr                    3.1.1     2018-12-21 [1] CRAN (R 3.5.1)
##  cli                      1.0.1     2018-09-25 [1] CRAN (R 3.5.1)
##  codetools                0.2-16    2018-12-24 [1] CRAN (R 3.5.1)
##  colorspace               1.3-2     2016-12-14 [1] CRAN (R 3.5.1)
##  crayon                   1.3.4     2017-09-16 [1] CRAN (R 3.5.1)
##  data.table               1.11.8    2018-09-30 [1] CRAN (R 3.5.1)
##  DBI                      1.0.0     2018-05-02 [1] CRAN (R 3.5.1)
##  DelayedArray           * 0.6.6     2018-09-11 [1] Bioconductor  
##  DelayedMatrixStats       1.2.0     2018-10-04 [1] Bioconductor  
##  desc                     1.2.0     2018-05-01 [1] CRAN (R 3.5.1)
##  devtools                 2.0.1     2018-10-26 [1] CRAN (R 3.5.1)
##  digest                   0.6.18    2018-10-10 [1] CRAN (R 3.5.1)
##  dmrseq                 * 1.0.14    2018-08-07 [1] Bioconductor  
##  doRNG                    1.7.1     2018-06-22 [1] CRAN (R 3.5.1)
##  dplyr                    0.7.8     2018-11-10 [1] CRAN (R 3.5.1)
##  evaluate                 0.12      2018-10-09 [1] CRAN (R 3.5.1)
##  foreach                  1.4.4     2017-12-12 [1] CRAN (R 3.5.1)
##  fs                       1.2.6     2018-08-23 [1] CRAN (R 3.5.1)
##  GenomeInfoDb           * 1.16.0    2018-10-04 [1] Bioconductor  
##  GenomeInfoDbData         1.1.0     2018-10-04 [1] Bioconductor  
##  GenomicAlignments        1.16.0    2018-10-04 [1] Bioconductor  
##  GenomicFeatures          1.32.3    2018-10-05 [1] Bioconductor  
##  GenomicRanges          * 1.32.7    2018-09-20 [1] Bioconductor  
##  ggplot2                  3.1.0     2018-10-25 [1] CRAN (R 3.5.1)
##  glue                     1.3.0     2018-07-17 [1] CRAN (R 3.5.1)
##  gtable                   0.2.0     2016-02-26 [1] CRAN (R 3.5.1)
##  gtools                   3.8.1     2018-06-26 [1] CRAN (R 3.5.1)
##  HDF5Array                1.8.1     2018-06-21 [1] Bioconductor  
##  hms                      0.4.2     2018-03-10 [1] CRAN (R 3.5.1)
##  htmltools                0.3.6     2017-04-28 [1] CRAN (R 3.5.1)
##  httpuv                   1.4.5.1   2018-12-18 [1] CRAN (R 3.5.1)
##  httr                     1.4.0     2018-12-11 [1] CRAN (R 3.5.1)
##  interactiveDisplayBase   1.18.0    2018-10-04 [1] Bioconductor  
##  IRanges                * 2.14.12   2018-09-20 [1] Bioconductor  
##  iterators                1.0.10    2018-07-13 [1] CRAN (R 3.5.1)
##  knitr                    1.21      2018-12-10 [1] CRAN (R 3.5.1)
##  later                    0.7.5     2018-09-18 [1] CRAN (R 3.5.1)
##  lattice                  0.20-38   2018-11-04 [1] CRAN (R 3.5.1)
##  lazyeval                 0.2.1     2017-10-29 [1] CRAN (R 3.5.1)
##  limma                    3.36.5    2018-09-20 [1] Bioconductor  
##  locfit                   1.5-9.1   2013-04-20 [1] CRAN (R 3.5.1)
##  magrittr                 1.5       2014-11-22 [1] CRAN (R 3.5.1)
##  Matrix                   1.2-15    2018-11-01 [1] CRAN (R 3.5.1)
##  matrixStats            * 0.54.0    2018-07-23 [1] CRAN (R 3.5.1)
##  memoise                  1.1.0     2017-04-21 [1] CRAN (R 3.5.1)
##  mime                     0.6       2018-10-05 [1] CRAN (R 3.5.1)
##  munsell                  0.5.0     2018-06-12 [1] CRAN (R 3.5.1)
##  nlme                     3.1-137   2018-04-07 [1] CRAN (R 3.5.1)
##  outliers                 0.14      2011-01-24 [1] CRAN (R 3.5.1)
##  permute                  0.9-4     2016-09-09 [1] CRAN (R 3.5.1)
##  pillar                   1.3.1     2018-12-15 [1] CRAN (R 3.5.1)
##  pkgbuild                 1.0.2     2018-10-16 [1] CRAN (R 3.5.1)
##  pkgconfig                2.0.2     2018-08-16 [1] CRAN (R 3.5.1)
##  pkgload                  1.0.2     2018-10-29 [1] CRAN (R 3.5.1)
##  pkgmaker                 0.27      2018-05-25 [1] CRAN (R 3.5.1)
##  plyr                     1.8.4     2016-06-08 [1] CRAN (R 3.5.1)
##  prettyunits              1.0.2     2015-07-13 [1] CRAN (R 3.5.1)
##  processx                 3.2.1     2018-12-05 [1] CRAN (R 3.5.1)
##  progress                 1.2.0     2018-06-14 [1] CRAN (R 3.5.1)
##  promises                 1.0.1     2018-04-13 [1] CRAN (R 3.5.1)
##  ps                       1.3.0     2018-12-21 [1] CRAN (R 3.5.1)
##  purrr                    0.2.5     2018-05-29 [1] CRAN (R 3.5.1)
##  R.methodsS3              1.7.1     2016-02-16 [1] CRAN (R 3.5.1)
##  R.oo                     1.22.0    2018-04-22 [1] CRAN (R 3.5.1)
##  R.utils                  2.7.0     2018-08-27 [1] CRAN (R 3.5.1)
##  R6                       2.3.0     2018-10-04 [1] CRAN (R 3.5.1)
##  RColorBrewer             1.1-2     2014-12-07 [1] CRAN (R 3.5.1)
##  Rcpp                     1.0.0     2018-11-07 [1] CRAN (R 3.5.1)
##  RCurl                    1.95-4.11 2018-07-15 [1] CRAN (R 3.5.1)
##  readr                    1.3.1     2018-12-21 [1] CRAN (R 3.5.1)
##  regioneR                 1.12.0    2018-10-04 [1] Bioconductor  
##  registry                 0.5       2017-12-03 [1] CRAN (R 3.5.1)
##  remotes                  2.0.2     2018-10-30 [1] CRAN (R 3.5.1)
##  reshape2                 1.4.3     2017-12-11 [1] CRAN (R 3.5.1)
##  rhdf5                    2.24.0    2018-10-04 [1] Bioconductor  
##  Rhdf5lib                 1.2.1     2018-10-04 [1] Bioconductor  
##  rlang                    0.3.0.1   2018-10-25 [1] CRAN (R 3.5.1)
##  rmarkdown                1.11      2018-12-08 [1] CRAN (R 3.5.1)
##  rngtools                 1.3.1     2018-05-15 [1] CRAN (R 3.5.1)
##  rprojroot                1.3-2     2018-01-03 [1] CRAN (R 3.5.1)
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## 
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library

DMRs: DMRs plots

Deepak Tanwar & Hana Parizkova

Created on: 2018-12-30
Updated on: 2019-01-07

1 Packages required

2 BSseq objects

2.1 Negative control

2.2 Simulated data

3 DMR files

3.1 Negative control

3.2 Simulated data

4 Annotation Human Genome

6 SessionInfo

DMRs: DMRs plots

Deepak Tanwar & Hana Parizkova

Created on: 2018-12-30 Updated on: 2019-01-07

1 Packages required

2 BSseq objects

2.1 Negative control

2.2 Simulated data

3 DMR files

3.1 Negative control

3.2 Simulated data

4 Annotation Human Genome

5 Regions plot Simulated data

5.1 Region1: delta 0.447

5.2 Region2: delta 0.44

5.3 Region3: delta 0.433

5.4 Region4: delta 0.425

5.5 Region5: delta 0.42

5.6 Region6: delta 0.42

5.7 Region7: delta 0.414

5.8 Region8: delta 0.413

5.9 Region9: delta 0.399

5.10 Region10: delta 0.39

5.11 Region11: delta 0.39

5.12 Region12: delta 0.389

5.13 Region13: delta 0.387

5.14 Region14: delta 0.383

5.15 Region15: delta 0.382

5.16 Region16: delta 0.379

5.17 Region17: delta 0.378

5.18 Region18: delta 0.374

5.19 Region19: delta 0.372

5.20 Region20: delta 0.372

5.21 Region21: delta 0.372

5.22 Region22: delta 0.37

5.23 Region23: delta 0.364

5.24 Region24: delta 0.36

5.25 Region25: delta 0.359

5.26 Region26: delta 0.357

5.27 Region27: delta 0.353

5.28 Region28: delta 0.345

5.29 Region29: delta 0.344

5.30 Region30: delta 0.339

5.31 Region31: delta 0.339

5.32 Region32: delta 0.333

5.33 Region33: delta 0.329

5.34 Region34: delta 0.328

5.35 Region35: delta 0.327

5.36 Region36: delta 0.324

5.37 Region37: delta 0.322

5.38 Region38: delta 0.322

5.39 Region39: delta 0.322

5.40 Region40: delta 0.319

5.41 Region41: delta 0.319

5.42 Region42: delta 0.318

5.43 Region43: delta 0.318

5.44 Region44: delta 0.317

5.45 Region45: delta 0.314

5.46 Region46: delta 0.313

5.47 Region47: delta 0.313

5.48 Region48: delta 0.312

5.49 Region49: delta 0.312

5.50 Region50: delta 0.306

5.51 Region51: delta 0.306

5.52 Region52: delta 0.305

5.53 Region53: delta 0.303

5.54 Region54: delta 0.303

5.55 Region55: delta 0.298

5.56 Region56: delta 0.296

5.57 Region57: delta 0.295

5.58 Region58: delta 0.295

5.59 Region59: delta 0.294

5.60 Region60: delta 0.292

5.61 Region61: delta 0.291

5.62 Region62: delta 0.29

5.63 Region63: delta 0.289

5.64 Region64: delta 0.277

5.65 Region65: delta 0.276

5.66 Region66: delta 0.275

5.67 Region67: delta 0.275

5.68 Region68: delta 0.274

Created on: 2018-12-30
Updated on: 2019-01-07